[gmx-users] start gromacs membrane more protein simulation

Andrey V. Golovin golovin at genebee.msu.su
Wed Sep 21 11:32:25 CEST 2005

you can try gendox -cs dppc128.pdb
but first you have to orient your protein properly in box

Antonio Sergio Kimus Braz wrote:
> Hi,
> I am beginner in the GROMACS
> I am trying to simulate a theorical model of a pump protein in explicit  
> lipid bilayer membrane environment (DMPC or POPC), I have the pdb
> files of this protein and membrane , I have to topolies files this
> lipids (dmpc.ip or popc.itp)…I also saw  the mdrun_make_hole.tar.gz in
> (http://www.gromacs.org/contributions/index.php) ..
> However my doubt stays, 
> n which stage I do enter with membrane files? pdb and itp.
> don't get to generate files type .gro or .top, starting from the
> membrane alone or membrane more protein pdb files, using pdb2gmx or
> editconf commands…
> I also tried to insert the membrane using the genbox command with –ci
> option with dmpc.pdb
> I don't really know as creating an input files membrane + protein for
> run in gromacs…
> Anybody could help ?
> thank you very much !
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Andrey V. Golovin
Ph.D,Professor assistant    tel: (095) 939-5305
Bioengineering and
Bioinformatics Department
Moscow State University     fax: (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su

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